On Sub-Atomic Nanogenes and the Realities That Bind Us

by JustAnotherFillyAuthor

Chapter 1

Her vision came back first, slowly but surely. Her peripherals were a blurry monochromatic mess, her head was pounding, and her vision swam with electric sparks ricocheting off the edges inside her skull like acid raindrops on limestone pavement.

She slowly raised her head, inhaled a shaky breath that pressed against her sternum in an odd fashion she couldn’t quite identify, and shook the cobwebs from her mind in a daze. As awareness reawakened her, she found herself lying on her back at the base of a vibrant green hill, staring at the breaking dawn above. A small body of water glittered a few feet away, and the trees swayed lightly in the breeze.

Wait.

She looked down at her arms. Pure white fur glistened with morning dew, and she stared at her hooves as something unfamiliar gnawed at the back of her mind.

This was wrong. Why was this wrong? She didn’t have hooves, did she? What was she? What was she before?

Suddenly, a sharp pain jolted through her skull.

“You can’t do this to me!” The young woman cried. Her screams echoed in the pale blue chamber she was housed in, an assortment of medical needles and hoses poking through her skin and holding her captive, floating in an iridescent liquid. Her breathing laboured as she took in more of the solution, each breath coating her burning lungs in chilling moisture. The veins in her pale skin throbbed angrily with each new substance injected into her, and she curled her quickly numbing fingers to bring the sensation back to them. Looking up, she glared at the sinister face staring back at her through the glass.

“Think of the sacrifices you’re making for humanity, my dear,” the man chuffed as he tugged at the lapels of his white lab coat, stained with sickeningly yellow marks around the neckline, “and just imagine how much better you will feel after this!” He straightened his coat, brushing off an old nametag from the front, bearing the name of ‘Cosmo Flaherty’ in brilliant gold lettering. Cosmo stroked the glass affectionately before making his way to a collection of vials on the table beside him. He held one up to the bright cold ceiling light, and it shone unnaturally.

She reeled back in horror, clutching at her head with her hands – no, hooves – and crying in alarm. This was not her body; she must be dreaming. She must be hallucinating. Her sluggish mind was racing to make sense of her surroundings. What was she doing here? What was she? Who was she? What was her name?

She did not remember anything.

The realization hit her like a freight-train, and she scrambled to her feet – hooves – kicking up too much dust in the process. She struggled to contain a cough as she made her way to the lake in a mad scramble and looked at her reflection.

A strange creature stared back at her; huge brown eyes wild and afraid, white pointy ears laid flat against her head, deep brown and blue mane long and untamed. The muzzle on the strange face wrinkled in confusion, and tears began to well in her eyes and dribble down her face, leaving tearstained marks. The reflection wobbled as her tears hit the pond, spilling ripples across her unfamiliar features.

This was not her – staring back at her was a pony. A white-furred, brown-and-blue-maned, chocolate-eyed mare.

She screamed, backing away madly from her distorted reflection. She turned and ran from the lake, stumbling blindly over her new hooves. Not bothering to swallow the panic in her throat. Her lungs burned and the world around her swam with unshed tears. She did not know where she was running, but she knew that she was running from something beyond her understanding. Her mind was racing faster than her hooves, and her brain felt searing hot despite the fog.

Something was very, very wrong.

As she galloped further and further from where she first woke up, the world became a blur through snot and tears she could not hold back. Emerald grass collided with turquoise sky in a whirlwind of panic as the mare raced through the field, unaware of anything around her but the primal instinct at the back of her mind telling her to run, you are in danger; run as fast as you can! Searing pain shot through her skull like an angry bullet with each step and grainy despondent images of another time swam unprovoked in her mind’s eye as she stumbled with the pain.

An image of a sterile white room, a flash of blinding lights, a metallic taste in her mouth as liquid fire flowed in her veins.

She was human! At least, she thought she was human.

She stumbled as another, clearer vision exploded in her head.

“Please, stop! I live alone and I have a cat, she needs someone to take care of her!” She cried, encased in the glass tube. Cosmo inserted a bright blue liquid into the I.V. drip inserted in her left arm and she gurgled in pain as something white-hot and angry entered her bloodstream. She could feel something crawling inside her veins, taking shape, traveling through her body, clawing at her lungs and latching into her heart and brain. She screamed in terror, thrashing about in the tank as her muscles spasmed violently.

“These nanogenes,” Cosmo muttered, ignoring his subject, “are programmed to rewire your mind. Produce more neurons, act as neural gateways for your currently vacant brain. They will learn your genetic code, recalling all of what you are within their tiny little computer minds, and they will protect you from harm. Just give them time to adjust.” He knocked a pile of research papers off his desk to make room for the beaker he was holding, and he picked up a pen before scribbling something down on a rogue sheet of paper.

“Why are you doing this to me? Please, let me go!” She begged, her heart racing uncontrollably as every organ and muscle burned with the energy of Cosmo’s experiment. Her voice came out as a choke, the liquid in the tank suppressing most of her voice.

“#040496; you and I will find the meaning of life together.”

The mare growled, gnawing at her lip to keep more tears from spilling. Her entire body burned as if fire was running through her veins, and now she remembered why. Her hooves were on fire and her veins were aflame as fury and fear in equal measure collided like wild vicious animals in her brain.

At the back of her mind, she went over the event; she was human – yes – and she was called #040496. That didn’t sound right to her, though. Why couldn’t she recall her name? Why couldn’t she recall anything?

Her new hooves crumbled under her, and she stumbled into the grass, tears welling in her eyes like a dam fit to burst. Unable to hold back her cries, the silence of the morning was broken with an almighty scream, and she sobbed bitterly into her muddy forelegs. She felt the visceral wrongness of how her tear-streaked muzzle felt as she rubbed it against her unfamiliar limbs, and she cried harder, screeching in horrendous anguish. Confusion and fear coated her mind in a deep, dark fog like an afternoon thunderstorm, and hordes of irate and fearful thoughts leapt unbidden from the depths, crashing angrily against her skull and flooding her furry ears.

Waves upon waves of bitter despair crashed onto her tiny frame, chilling her bones and anchoring her to the ground as she finally collapsed under the almighty weight of emotions beating down upon her. She couldn't take it any more.

She closed her eyes, yet she still saw the clear, cold, glinting eyes of the man that did this to her. His indifferent sneer burned into her brain and mocked her slipping sanity. She cried out in fear once more, burying her head in her hooves and curling up defensively in a feeble and fruitless attempt to keep the internal attack at bay.

What was wrong with her?

All she could see in her mind’s eye was a fragile memory of an identification number. She was #040496. She was #040496.
She was #040496.
The poisonous mantra rang in her skull and crashed violently against her burning heart, and she sobbed uncontrollably into her new hooves.

---

There was a disturbance. He could feel it in his bones, in his ever-racing mind. The energy in the air was almost tangible, and the taste of iron and electricity prickled on his tongue, settling in his thick chocolate fur like a deadly poison.

With head turned to the late afternoon sun beating down on him like a stifling, brilliant omen, the stallion grew rigid, inhaling deeply.

His companion stopped in her tracks, seeing that he had done the same.

“What’s the matter, Doctor? Is something wrong?” The blonde pony asked in a soft tone, her head tilted slightly. Her golden eyes were crossed, one holding the stallion’s own gaze and the other looking to her left, unseeing, unmoving.

The stallion took a moment to give his companion a reassuring grin before shaking his head. He shrugged off the feeling and turned back to the skies, breaking eye contact with the mare.

“No. No, it’s fine, Ditzy. There’s something in the air, though. I can feel it.” The Doctor murmured, staring at the arching streaks of light sunbeams. Ditzy looked at the sky but could only guess as to what her friend was talking about. She had learned long ago not to question the Doctor’s logic. Instead, she fluffed out her wings and turned back to the road.

“Well then,” She began, taking a few cautious steps forward, “Let’s get going!”

The Doctor responded with a noncommittal hum, his mind somewhere else entirely. Uncertainty prickled at him as a familiar anxiety settled into his skin. He had seen too much and had been alive for too long to brush off the sense of carnal uncertainty that had taken hold of him; the universe had shifted skeins, and something was different in this universe now.

Whatever it was; if it was to be a problem, he would have to solve it.

Author's Note:

This story is fully written. I will be proofreading each chapter and uploading them one by one over the course of the next several weeks once I am happy with the results.

This fic is well over 100k words and I have enjoyed writing every single bit of it, so I really hope you enjoy my work. :-)